Hi Michael,

No, they were sequenced from different places. So, you don't recommend to
use DESeq to do the analysis?

Ben


On Wed, Aug 6, 2014 at 12:03 PM, Michael Love <michaelisaiahlove@gmail.com>
wrote:

> hi Ben,
>
> One problem with this comparison is that, without replicates from at
> least one site, the statistical methods have no way of assessing the
> biological and technical variability of the experiment. Just like with
> a t-test, the question, is 2 < 6 depends on how much variability we
> expect from sampling again and again. For more information, read the
> paragraph "Experiments without replicates..." in ?DESeq.
>
> were the samples from the different sites prepared and sequenced at
> the same facility?
>
> as far as technical aspects of using DESeq/edgeR for metagenomics,
> Joey McMurdie has comprehensive instructions here:
> http://joey711.github.io/phyloseq/
>
> Mike
>
> On Wed, Aug 6, 2014 at 1:42 PM, Pet Chiang <sdpapet@gmail.com> wrote:
> >  I am working on my metagenomic data sets.
> >
> > I have annotated my metagenome against COG database. I would like to use
> > DESeq to look for the overabundant genes in my site.
> >
> > Here is the problem, I only have one site (one metagenome). I would like
> to
> > compare this one to different sites (each of these site has no
> replication
> > too)
> >
> > the count data set looks like this:
> >
> >  function name                my site      site1 (from US)    site 2
> (from
> > Japan)  site (from Iceland) .....
> > COG1                                 2(counts)    6
> > 9                         9
> > COG2                                 5
> > 5                        8                          8
> > COG3                                 7
> > 9                        8                             0
> > .....
> >
> > I want to find if any of COG functions in my site is over-representative,
> > which means the functional gene counts are overabundant across other
> sites.
> >
> > However, I am not sure  DESeq can do this or not?
> >
> > If it can do this, how can I set the groups.
> >
> > Best regards,
> > Ben
> >
> >         [[alternative HTML version deleted]]
> >
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